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Table S1. Descriptions of the ten investigated nuclear loci.

Table S2. Primers used for mtDNA and cpDNA amplification. Primers that generated polymorphic cpSSR sites are in bold.

Table S3. Prior distribution of the demographic parameters for standard neutral model (N), exponential growth model (G), and bottleneck model (B).

Table S4. Geographic location, sample sizes (N), the number of segregating sites (S), nucleotide polymorphism (θw), nucleotide diversity (πt, total sites; πs, silent sites; πa, nonsynonymous), number of haplotypes (nh) of the investigated populations of P. krempfii based on individual nuclear loci.

Table S5. Neutrality tests for individual nuclear loci as measured by Tajima's D, Fu and Li's D* and F*, Fu's Fs, standardized Fay and Wu's H, and the MK test.

Table S6. Population differentiation (FST) for each region and total sample of P. krempfii based on individual and combined nuclear loci.

Table S7. Summary of nucleotide diversity and effective population size in 22 pine species based on nuclear genes. Species with limited range of distribution are in bold.

Figure S1. Linkage disequilibrium (r2) as a function of the distance between sites across the ten nuclear genes in P. krempfii.

Figure S2. Structure analysis of the six sampled populations of P. krempfii based on nuclear loci. (a) The log probability of data L(K) (mean and standard deviation over 10 replicates) given the number of genetic clusters K ranging between 1 and 10. (b) Magnitude of ΔK for each = 2–9. (c) Assignments of population frequency of demes by structure at = 2–6. For each K value, results of the run with the highest value of L(K) were used.

Figure S3. Mean and variance of four summary statistics calculated from 105 posterior predictive simulations. Values of the corresponding summary statistics for the observed nuclear data are indicated by vertical red lines.

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